1JVAA

Crystal structure of the vma1-derived endonuclease bearing the n and c extein propeptides
Total Genus 117
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
117
sequence length
460
structure length
427
Chain Sequence
VGSFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSEVPELLKFTCNATNELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVTEYAEKLNLCAEYKDRKEPQVAKTVNLYSKVENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVVSVNAEPKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLSDDSDHQFLLANQVVVHSSGER
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule tags Hydrolase
molecule keywords VMA1-DERIVED HOMING ENDONUCLEASE X10SSS
publication title Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides.
pubmed doi rcsb
source organism Saccharomyces cerevisiae
total genus 117
structure length 427
sequence length 460
chains with identical sequence B
ec nomenclature ec 7.1.2.2: H(+)-transporting two-sector ATPase.
pdb deposition date 2001-08-29

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF05203 Hom_end_hint Hom_end-associated Hint
A PF05204 Hom_end Homing endonuclease
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.170.16.10 Mainly Beta Beta Complex Endonuclease - Pi-scei; Chain A, domain 1 Hedgehog/Intein (Hint) domain 1jvaA01
3.10.28.10 Alpha Beta Roll Endonuclease I-creI Homing endonucleases 1jvaA02
3.10.28.10 Alpha Beta Roll Endonuclease I-creI Homing endonucleases 1jvaA03
5AKMA 4UN9A 3OOLA 4OZ6A 1BP7A 5E63A 5E67A 3MXAA 5A78A 1U0CA 5A0MB 1G9YA 4AAFA 2DCHX 2FLDA 4LQ0A 4UN7G 1B24A 4E2UA 3NZMA 2IN8A 2LQMA 2VS7A 3E54A 4YISA 2XE0A 4UNCA 2VBLB 1LWTA 4AAEA 5AKFA 1AF5A 4Z1ZA 2L8LA 5A0WA 2VBOA 5AKNA 4GIGA 4EFJA 3UVFA 2LWYA 1G9ZA 4Z1XA 1EF0A 4UN9G 1N3FA 2EX5A 1R7MA 5E5SA 4UN8A 2I3QA 1GPPA 4KL5A 3MX9A 4AABA 2AB5A 1VDEA 1AT0A 3QQYA 2VBNA 4YHXA 5E5OA 3KO2A 1P8KZ 3HYIA 1U0DA 1M5XA 4AAGA 3FD2A 1AM2A 5A72A 4KL6A 2QOJZ 2XE0B 1DQ3A 2VBJA 1DFAA 4AADA 1ZD7A 3MISA 4D6NA 2VBOB 3MXBB 4UN8G 1LWSA 4D6OA 4UNAA 2O7MA 5K08A 4AQXA 1JVAA 3C0XA 1ZDEA 2IN0A 4YITA 5AK9A 2IN9A 2JNQA 5A0MA 5I0AA 4UNBA 3HYJA 2VBNB 3OORA 3EH8A 4E2TA 3IFJA 5A74A 4UT0A 1MOWA 2VBLA 4AQUA 4O1SA 4UN7A 4Z20A 3C0WA 2VS8A 1N3EA 3IGDA 5A77A 4O1RA 2VBJB 1T9JA 1T9IA 2LCJA 2JMZA 3MIPA 3R7PA 2I3PA 4LOXA 2CW8A 2IMZA 2CW7A 2KEQA 3MXBA 1UM2A 1MI8A
chains in the Genus database with same CATH superfamily
5AKMA 4UN9A 3OOLA 4OZ6A 1BP7A 5E63A 5E67A 3MXAA 5A78A 1U0CA 5A0MB 1G9YA 4AAFA 2DCHX 2FLDA 4LQ0A 4UN7G 1B24A 4E2UA 3NZMA 2IN8A 2LQMA 2VS7A 3E54A 4YISA 2XE0A 4UNCA 2F4LA 2VBLB 1LWTA 4AAEA 5AKFA 1AF5A 4Z1ZA 2L8LA 5A0WA 2VBOA 5AKNA 4GIGA 4EFJA 3UVFA 2LWYA 1G9ZA 4Z1XA 1EF0A 4UN9G 1N3FA 2EX5A 1R7MA 5E5SA 4UN8A 2I3QA 1GPPA 4KL5A 3MX9A 4KZSA 2AB5A 1VDEA 4AABA 1AT0A 3QQYA 2VBNA 4YHXA 4LX3A 5E5OA 3KO2A 1P8KZ 3HYIA 1U0DA 1M5XA 4AAGA 3FD2A 1AM2A 5A72A 4KL6A 2QOJZ 2XE0B 1DQ3A 2VBJA 1DFAA 4AADA 1ZD7A 3MISA 4D6NA 2VBOB 3MXBB 4UN8G 1LWSA 4D6OA 4UNAA 2O7MA 4QFQA 5K08A 4AQXA 1JVAA 3C0XA 1ZDEA 2IN0A 4YITA 5AK9A 2IN9A 2JNQA 5A0MA 5I0AA 4UNBA 3HYJA 2VBNB 3OORA 3EH8A 4E2TA 3IFJA 5A74A 4UT0A 1MOWA 2VBLA 4AQUA 4O1SA 4UN7A 4Z20A 3C0WA 2VS8A 1N3EA 3IGDA 5A77A 4O1RA 2VBJB 1T9JA 1T9IA 2LCJA 2JMZA 3MIPA 3R7PA 2I3PA 4LOXA 2CW8A 2IMZA 2CW7A 2KEQA 3MXBA 1UM2A 1MI8A
chains in the Genus database with same CATH topology
5AKMA 4UN9A 3OOLA 4OZ6A 1BP7A 5E63A 5E67A 3MXAA 5A78A 1U0CA 5A0MB 1G9YA 4AAFA 2DCHX 2FLDA 4LQ0A 4UN7G 1B24A 4E2UA 3NZMA 2IN8A 2LQMA 2VS7A 3E54A 4YISA 2XE0A 4UNCA 2VBLB 1LWTA 4AAEA 5AKFA 1AF5A 4Z1ZA 2L8LA 5A0WA 2VBOA 5AKNA 4GIGA 4EFJA 3UVFA 2LWYA 1G9ZA 4Z1XA 1EF0A 4UN9G 1N3FA 2EX5A 1R7MA 5E5SA 4UN8A 2I3QA 1GPPA 4KL5A 3MX9A 4AABA 2AB5A 1VDEA 1AT0A 3QQYA 2VBNA 4YHXA 5E5OA 3KO2A 1P8KZ 3HYIA 1U0DA 1M5XA 4AAGA 3FD2A 1AM2A 5A72A 4KL6A 2QOJZ 2XE0B 1DQ3A 2VBJA 1DFAA 4AADA 1ZD7A 3MISA 4D6NA 2VBOB 3MXBB 4UN8G 1LWSA 4D6OA 4UNAA 2O7MA 5K08A 4AQXA 1JVAA 3C0XA 1ZDEA 2IN0A 4YITA 5AK9A 2IN9A 2JNQA 5A0MA 5I0AA 4UNBA 3HYJA 2VBNB 3OORA 3EH8A 4E2TA 3IFJA 5A74A 4UT0A 1MOWA 2VBLA 4AQUA 4O1SA 4UN7A 4Z20A 3C0WA 2VS8A 1N3EA 3IGDA 5A77A 4O1RA 2VBJB 1T9JA 1T9IA 2LCJA 2JMZA 3MIPA 3R7PA 2I3PA 4LOXA 2CW8A 2IMZA 2CW7A 2KEQA 3MXBA 1UM2A 1MI8A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 5AKM A;  4UN9 A;  3OOL A;  4OZ6 A;  1BP7 A;  5E63 A;  5E67 A;  3MXA A;  5A78 A;  1U0C A;  5A0M B;  1G9Y A;  4AAF A;  2DCH X;  2FLD A;  4LQ0 A;  4UN7 G;  1B24 A;  4E2U A;  3NZM A;  2IN8 A;  2LQM A;  2VS7 A;  3E54 A;  4YIS A;  2XE0 A;  4UNC A;  2VBL B;  1LWT A;  4AAE A;  5AKF A;  1AF5 A;  4Z1Z A;  2L8L A;  5A0W A;  2VBO A;  5AKN A;  4GIG A;  4EFJ A;  3UVF A;  2LWY A;  1G9Z A;  4Z1X A;  1EF0 A;  4UN9 G;  1N3F A;  2EX5 A;  1R7M A;  5E5S A;  4UN8 A;  2I3Q A;  1GPP A;  4KL5 A;  3MX9 A;  4AAB A;  2AB5 A;  1VDE A;  1AT0 A;  3QQY A;  2VBN A;  4YHX A;  5E5O A;  3KO2 A;  1P8K Z;  3HYI A;  1U0D A;  1M5X A;  4AAG A;  3FD2 A;  1AM2 A;  5A72 A;  4KL6 A;  2QOJ Z;  2XE0 B;  1DQ3 A;  2VBJ A;  1DFA A;  4AAD A;  1ZD7 A;  3MIS A;  4D6N A;  2VBO B;  3MXB B;  4UN8 G;  1LWS A;  4D6O A;  4UNA A;  2O7M A;  5K08 A;  4AQX A;  1JVA A;  3C0X A;  1ZDE A;  2IN0 A;  4YIT A;  5AK9 A;  2IN9 A;  2JNQ A;  5A0M A;  5I0A A;  4UNB A;  3HYJ A;  2VBN B;  3OOR A;  3EH8 A;  4E2T A;  3IFJ A;  5A74 A;  4UT0 A;  1MOW A;  2VBL A;  4AQU A;  4O1S A;  4UN7 A;  4Z20 A;  3C0W A;  2VS8 A;  1N3E A;  3IGD A;  5A77 A;  4O1R A;  2VBJ B;  1T9J A;  1T9I A;  2LCJ A;  2JMZ A;  3MIP A;  3R7P A;  2I3P A;  4LOX A;  2CW8 A;  2IMZ A;  2CW7 A;  2KEQ A;  3MXB A;  1UM2 A;  1MI8 A; 
#chains in the Genus database with same CATH topology
 5AKM A;  4UN9 A;  3OOL A;  4OZ6 A;  1BP7 A;  5E63 A;  5E67 A;  3MXA A;  5A78 A;  1U0C A;  5A0M B;  1G9Y A;  4AAF A;  2DCH X;  2FLD A;  4LQ0 A;  4UN7 G;  1B24 A;  4E2U A;  3NZM A;  2IN8 A;  2LQM A;  2VS7 A;  3E54 A;  4YIS A;  2XE0 A;  4UNC A;  2F4L A;  2VBL B;  1LWT A;  4AAE A;  5AKF A;  1AF5 A;  4Z1Z A;  2L8L A;  5A0W A;  2VBO A;  5AKN A;  4GIG A;  4EFJ A;  3UVF A;  2LWY A;  1G9Z A;  4Z1X A;  1EF0 A;  4UN9 G;  1N3F A;  2EX5 A;  1R7M A;  5E5S A;  4UN8 A;  2I3Q A;  1GPP A;  4KL5 A;  3MX9 A;  4KZS A;  2AB5 A;  1VDE A;  4AAB A;  1AT0 A;  3QQY A;  2VBN A;  4YHX A;  4LX3 A;  5E5O A;  3KO2 A;  1P8K Z;  3HYI A;  1U0D A;  1M5X A;  4AAG A;  3FD2 A;  1AM2 A;  5A72 A;  4KL6 A;  2QOJ Z;  2XE0 B;  1DQ3 A;  2VBJ A;  1DFA A;  4AAD A;  1ZD7 A;  3MIS A;  4D6N A;  2VBO B;  3MXB B;  4UN8 G;  1LWS A;  4D6O A;  4UNA A;  2O7M A;  4QFQ A;  5K08 A;  4AQX A;  1JVA A;  3C0X A;  1ZDE A;  2IN0 A;  4YIT A;  5AK9 A;  2IN9 A;  2JNQ A;  5A0M A;  5I0A A;  4UNB A;  3HYJ A;  2VBN B;  3OOR A;  3EH8 A;  4E2T A;  3IFJ A;  5A74 A;  4UT0 A;  1MOW A;  2VBL A;  4AQU A;  4O1S A;  4UN7 A;  4Z20 A;  3C0W A;  2VS8 A;  1N3E A;  3IGD A;  5A77 A;  4O1R A;  2VBJ B;  1T9J A;  1T9I A;  2LCJ A;  2JMZ A;  3MIP A;  3R7P A;  2I3P A;  4LOX A;  2CW8 A;  2IMZ A;  2CW7 A;  2KEQ A;  3MXB A;  1UM2 A;  1MI8 A; 
#chains in the Genus database with same CATH homology
 5AKM A;  4UN9 A;  3OOL A;  4OZ6 A;  1BP7 A;  5E63 A;  5E67 A;  3MXA A;  5A78 A;  1U0C A;  5A0M B;  1G9Y A;  4AAF A;  2DCH X;  2FLD A;  4LQ0 A;  4UN7 G;  1B24 A;  4E2U A;  3NZM A;  2IN8 A;  2LQM A;  2VS7 A;  3E54 A;  4YIS A;  2XE0 A;  4UNC A;  2VBL B;  1LWT A;  4AAE A;  5AKF A;  1AF5 A;  4Z1Z A;  2L8L A;  5A0W A;  2VBO A;  5AKN A;  4GIG A;  4EFJ A;  3UVF A;  2LWY A;  1G9Z A;  4Z1X A;  1EF0 A;  4UN9 G;  1N3F A;  2EX5 A;  1R7M A;  5E5S A;  4UN8 A;  2I3Q A;  1GPP A;  4KL5 A;  3MX9 A;  4AAB A;  2AB5 A;  1VDE A;  1AT0 A;  3QQY A;  2VBN A;  4YHX A;  5E5O A;  3KO2 A;  1P8K Z;  3HYI A;  1U0D A;  1M5X A;  4AAG A;  3FD2 A;  1AM2 A;  5A72 A;  4KL6 A;  2QOJ Z;  2XE0 B;  1DQ3 A;  2VBJ A;  1DFA A;  4AAD A;  1ZD7 A;  3MIS A;  4D6N A;  2VBO B;  3MXB B;  4UN8 G;  1LWS A;  4D6O A;  4UNA A;  2O7M A;  5K08 A;  4AQX A;  1JVA A;  3C0X A;  1ZDE A;  2IN0 A;  4YIT A;  5AK9 A;  2IN9 A;  2JNQ A;  5A0M A;  5I0A A;  4UNB A;  3HYJ A;  2VBN B;  3OOR A;  3EH8 A;  4E2T A;  3IFJ A;  5A74 A;  4UT0 A;  1MOW A;  2VBL A;  4AQU A;  4O1S A;  4UN7 A;  4Z20 A;  3C0W A;  2VS8 A;  1N3E A;  3IGD A;  5A77 A;  4O1R A;  2VBJ B;  1T9J A;  1T9I A;  2LCJ A;  2JMZ A;  3MIP A;  3R7P A;  2I3P A;  4LOX A;  2CW8 A;  2IMZ A;  2CW7 A;  2KEQ A;  3MXB A;  1UM2 A;  1MI8 A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
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